TY - JOUR

T1 - FISH Going Meso-Scale

T2 - A Microscopic Search for Chromatin Domains

AU - Maslova, Antonina

AU - Krasikova, Alla

N1 - Publisher Copyright: © Copyright © 2021 Maslova and Krasikova.

PY - 2021/11/3

Y1 - 2021/11/3

N2 - The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.

AB - The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.

KW - chromatin domains

KW - chromatin imaging

KW - FISH probes

KW - fluorescence in situ hybridization (FISH)

KW - fluorescent microscopy

KW - genome compartments

KW - Oligopaints

KW - topologically associating domains

KW - OLIGONUCLEOTIDE PROBES

KW - MOLECULE-LABELED NUCLEOTIDES

KW - 3D GENOME ARCHITECTURE

KW - IN-SITU HYBRIDIZATION

KW - COMPUTATIONAL METHODS

KW - INTERPHASE CHROMOSOMES

KW - HI-C

KW - DNA PROBES

KW - CHROMOSOME CONFORMATION CAPTURE

KW - 3-DIMENSIONAL ORGANIZATION

UR - http://www.scopus.com/inward/record.url?scp=85119407595&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/129e60ba-5b4b-3904-b85a-981ee7dd8072/

U2 - 10.3389/fcell.2021.753097

DO - 10.3389/fcell.2021.753097

M3 - Review article

AN - SCOPUS:85119407595

VL - 9

JO - Frontiers in Cell and Developmental Biology

JF - Frontiers in Cell and Developmental Biology

SN - 2296-634X

M1 - 753097

ER -